DESCRIPTION Crohn's disease is a remarkably prevalent and aggressive form of inflammatory bowel disease that often progresses to strictures, fistulas, and perforations requiring surgical intervention. Powerful immunosuppression and anti-inflammatory therapies have not altered the reliance on surgery, fueling the search for therapies that target the etiology of this condition. Major advances in genetics and pathophysiology in the past decade have now clearly established that Crohn's, and inflammatory bowel diseases in general, are pathologies in the management of gut microbes by the immediate epithelial lining and cells of the innate and adaptive immune system. Support for this notion comes from recent genome-wide association studies (GWAS) that, in addition to the expected immune regulatory genes, have implicated a vast network of genes linked to the intestinal epithelia. A major gap in our understanding the role of intestinal epithelia in Crohn's and other inflammatory bowel diseases has been the lack of robust in vitro cultivation systems to test epithelial function separate from confounding influences of the inflamed gut. We have now developed reliable technologies to clone so-called ?ground state? stem cells from each region of the human gastrointestinal tract and have shown them to possess epigenetic memory of and capacity for precise 3-D differentiation consistent with their origins despite months of continuous cultivation. This same technology now has been used to capture stem cells from endoscopic biopsies of Crohn's patients. Unexpectedly, biopsies from these patients yield two distinct populations of epithelial stem cells including one identical to those of control patients and another marked by a stable inflammatory gene signature and profound defects in the differentiation of secretory cell types. Significantly, we now have strong preliminary evidence that these two properties of the aberrant stem cells are the result of a profound epigenetic transformation of cells of the terminal ileum to those of proximal intestine. In three specific aims, we will test hypotheses that 1) this population of aberrant stem cells confers a mucosal hypersensitivity to microbial products, 2) that the combination of secreted chemokines and cytokines produced by these aberrant stem cells is sufficient to promote an inflammatory state in the mucosa, and 3), that the aberrant stem cells we identified in Crohn's represent a permanent and epigenetically enforced switch from a terminal ileum to a proximal intestine state and along with that switch both the hypersensitivity and proinflammatory phenotypes. We anticipate that these studies will provide novel insights into the cell biology of Crohn's, the role of mucosal stem cell heterogeneity in the pathological interactions between the immune system, the microbiome, and the intervening intestinal mucosa, and provide insights into potential therapeutic targets for the mitigation of this and inflammatory bowel diseases in general.